I'm primarily a self-taught programmer. I have taken a handful of classes, which is precisely why I'm pro teach yourself. Having a vision for what you want to create with code makes everything so much easier. Pseudo code So, you have some idea about what you want to program. Start by writing pseudo-code. This is… Continue reading How to teach yourself coding
This code introduces how to perform parameter estimation for a system of differential equations in R. First, the necessary packages and data are imported using code previously introduced in a previous post. R code available here. Due to computational constraints, the mathematical model we are using to fit to the data includes product inhibition. If product inhibition doesn't… Continue reading Introduction to modeling: parameter estimation in R
After introducing students to a simple mathematical model describing enzyme kinetics, I introduced them to coding and modeling in R. Coding is traditionally done by first describing some coding 'rules', including ending the line with semicolons or how to define a variable. Personally I found these methods ineffective and frustrating. I took a few classes… Continue reading Introduction to modeling and coding in R
Example code can be found on my github.
Here is powerpoint for teaching programming for mathematical biology. Referenced files are available on my github.
Programming elements that are used to perform basic mathematical calculations include: Arrays Matrices Equations or Simple functions Math functions See my previous post about the first two here. This post will deal with the latter two. Equations or Simple functions The simplest problem to be solved via programming would be the solution to a single… Continue reading Basic Mathematical Biology Programming Part II
Programming elements that are used to perform basic mathematical calculations include: Arrays Matrices Equations or Simple functions Math functions This post will deal with the first two. Arrays Sets are common in mathematical biology : response values, independent values, time units, gene or protein names. These sets can be expressed as arrays. The two most… Continue reading Basic Mathematical Biology Programming Part I